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From 2011.igem.org

6/4/11 - Today I learned how to make a basic GUI in java and use the text fields in this GUI to create format, person, and part objects using the Clotho core. I also learned how to save the part object to the database and make a basic status text label. Most of all though, I learned that it takes more than five minutes to write your first app.

6/5/11 - designed a preliminary GUI layout

6/6/11 - After boot camp, Jenhan taught me about BioFab and we discussed the separation between the BioFab IDE and the functionality of the tools. We think that this needs to be set in stone before we develop our tools, or else there will be compatibility issues between the iPhone style widget and BioFab.

6/7/11 - Today I implemented a search function in my PADS GUI. I'm currently trying to separate the returned collection by parts/formats/vectors etc. Most of my time has been spent learning layouts and swing. I'm also trying to generalize our permutation problem by looking for any modularity that might exist as the number of parts increases. Jenhan had the interesting idea that maybe, rather than find a general algorithm, we might need to find ways to optimize brute force methods of invertase placing...

6/8/11 - Implemented a dynamic tabbed search bar today based on the code from the BioFab's search tool. Jenhan and I are going to fix this up a little and replace the BioFab search with it. We thought this would not only be useful for the BioFab widget but that people could use it for other apps if necessary (I might use it in my PADS app). Also, Swapnil and I discussed a few different sorting methods that are similar to our invertase problem. I'm still trying to play with ideas and make generalizations. I think that these algorithms will be a good starting position.

6/9/11 - Finished the tabbed search today. Jenhan is going to integrate this search into the BioFab IDE. Also, I began categorizing and testing different invertase designs. Thus far, my categories include the following:

1. Protected Sites - placing invertases inside invertases in order to switch their directionality and continue to use them even though they flip.

 Benefits - reusable sites, might be most easily generalized
 Cons - requires extra invertases, requires more steps (added invertases) to get to certain permutations

2. Preemptive Sites - placing inverases such that they are NOT FACING THE CORRECT DIRECTION in anticipation of a flip that will give them the correct directionality.

 Pros - requires less sites than Protected Site Method
 Cons - probably harder to generalize than Protected Sites

3. Quick Start Sites - placing invertases such that any part in the design can be quickly moved to the starting position of the order. While testing different ideas, I found that the permutations that required the most invertases added (i.e. the most transformations) were those that placed the final part of the original design at the beginning of the design. For example, if our original part order is ABCD, permutations beginning with C and D required the most number of invertases to be added.

 Pros - might lower the number of transformations
 Cons - i haven't investigated this closely enough to specify the cons

If all of these categories can be generalized to an algorithm, our GUI could offer the user the ability to try different methods which might be interesting.

6/10/11 - Today I began working on an Invertase Simulator. It will take in your design and generate a list of permutations by trying every set of inputs (all permutations). I will update the notebook more when I make progress on this tool.